Commit c5642bbb by Eric Coissac

Change the awk call by $AwkCmd

parent 3ed87608
......@@ -61,7 +61,7 @@ function usage {
function fastaIterator() {
awk '/^>/ {if (seq) printf("%s\f",seq); seq=""} \
$AwkCmd '/^>/ {if (seq) printf("%s\f",seq); seq=""} \
{if (seq) seq=seq"\n"; seq=seq $1} \
END {print seq}' "$1"
}
......@@ -119,7 +119,7 @@ pushTmpDir ORG.organnot
if [[ ! -z "${sequence}" ]] ; then
echo "${sequence}" > toannotate.fasta
seqid=$(awk '(NR==1) {print substr($1,2,1000)}' toannotate.fasta)
seqid=$($AwkCmd '(NR==1) {print substr($1,2,1000)}' toannotate.fasta)
case "$types" in
chloro)
......@@ -246,17 +246,20 @@ pushTmpDir ORG.organnot
loginfo "Done."
loginfo "Ordering annotations..."
awk '/^.....(misc|repeat|rRNA|tRNA|gene|source)/ { \
$AwkCmd '(entry && /^.....(misc|repeat|rRNA|tRNA|gene|source)/) { \
print pos,entry } \
/^.....(misc|repeat|rRNA|tRNA|gene|source)/ { \
match($3,"[0-9][0-9]*"); \
pos=substr($3,RSTART,RLENGTH)*1000 + 1; \
print pos,$0; \
entry=$0; \
next} \
{ pos++; \
print pos,$0}' "${RESULTS}.annot" | \
{ entry=entry "@" $0} \
END {print pos,entry}' "${RESULTS}.annot" | \
sort -nk1 |\
awk '{ \
$AwkCmd '{ \
match($0,"^[0-9]* ");\
line=substr($0,RLENGTH+1);\
gsub("@","\n",line); \
print line}'
loginfo "Done."
......@@ -267,7 +270,7 @@ pushTmpDir ORG.organnot
loginfo "Done."
loginfo "Computing statistics on nucleotide usage..."
awk '! /^>/ { \
$AwkCmd '! /^>/ { \
seq=toupper($0); \
gsub(" ","",seq); \
lseq=length(seq); \
......@@ -293,8 +296,8 @@ pushTmpDir ORG.organnot
loginfo "Done."
loginfo "Reformating sequences..."
lines=$(wc -l "${RESULTS}.norm.fasta" | awk '{print $1}')
awk -v lines=$lines ' \
lines=$(wc -l "${RESULTS}.norm.fasta" | $AwkCmd '{print $1}')
$AwkCmd -v lines=$lines ' \
! /^>/ { \
seq=tolower($0); \
gsub(" ","",seq); \
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment